1
|
Furuya T, Saegusa N, Yamaoka S, Tomoita Y, Minamino N, Niwa M, Inoue K, Yamamoto C, Motomura K, Shimadzu S, Nishihama R, Ishizaki K, Ueda T, Fukaki H, Kohchi T, Fukuda H, Kasahara M, Araki T, Kondo Y. A non-canonical BZR/BES transcription factor regulates the development of haploid reproductive organs in Marchantia polymorpha. NATURE PLANTS 2024; 10:785-797. [PMID: 38605238 DOI: 10.1038/s41477-024-01669-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Gametogenesis, which is essential to the sexual reproductive system, has drastically changed during plant evolution. Bryophytes, lycophytes and ferns develop reproductive organs called gametangia-antheridia and archegonia for sperm and egg production, respectively. However, the molecular mechanism of early gametangium development remains unclear. Here we identified a 'non-canonical' type of BZR/BES transcription factor, MpBZR3, as a regulator of gametangium development in a model bryophyte, Marchantia polymorpha. Interestingly, overexpression of MpBZR3 induced ectopic gametangia. Genetic analysis revealed that MpBZR3 promotes the early phase of antheridium development in male plants. By contrast, MpBZR3 is required for the late phase of archegonium development in female plants. We demonstrate that MpBZR3 is necessary for the successful development of both antheridia and archegonia but functions in a different manner between the two sexes. Together, the functional specialization of this 'non-canonical' type of BZR/BES member may have contributed to the evolution of reproductive systems.
Collapse
Affiliation(s)
- Tomoyuki Furuya
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.
- Graduate School of Science, Kobe University, Kobe, Japan.
- Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Natsumi Saegusa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuki Tomoita
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Masaki Niwa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- GRA&GREEN Inc., Nagoya, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Chiaki Yamamoto
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Kazuki Motomura
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
- Japanese Science and Technology Agency, PRESTO, Kawaguchi, Japan
| | - Shunji Shimadzu
- Graduate School of Science, Kobe University, Kobe, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | | | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Japan
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroo Fukuda
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Faculty of Bioenvironmental Science, Kyoto University of Advanced Science, Kameoka, Japan
- Akita Prefectural University, Akita, Japan
| | | | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuki Kondo
- Graduate School of Science, Kobe University, Kobe, Japan.
- Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.
| |
Collapse
|
2
|
Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
Collapse
Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
3
|
Du P, Wang Q, Yuan D, Chen S, Su Y, Li L, Chen S, He X. WRKY transcription factors and OBERON histone-binding proteins form complexes to balance plant growth and stress tolerance. EMBO J 2023; 42:e113639. [PMID: 37565504 PMCID: PMC10548177 DOI: 10.15252/embj.2023113639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023] Open
Abstract
WRKY transcription factors in plants are known to be able to mediate either transcriptional activation or repression, but the mechanism regulating their transcriptional activity is largely unclear. We found that group IId WRKY transcription factors interact with OBERON (OBE) proteins, forming redundant WRKY-OBE complexes in Arabidopsis thaliana. The coiled-coil domain of WRKY transcription factors binds to OBE proteins and is responsible for target gene selection and transcriptional repression. The PHD finger of OBE proteins binds to both histones and WRKY transcription factors. WRKY-OBE complexes repress the transcription of numerous stress-responsive genes and are required for maintaining normal plant growth. Several WRKY and OBE mutants show reduced plant size and increased drought tolerance, accompanied by increased expression of stress-responsive genes. Moreover, expression levels of most of these WRKY and OBE genes are reduced in response to drought stress, revealing a previously uncharacterized regulatory mechanism of the drought stress response. These results suggest that WRKY-OBE complexes repress transcription of stress-responsive genes, and thereby balance plant growth and stress tolerance.
Collapse
Affiliation(s)
- Ping Du
- College of Life SciencesBeijing Normal UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
| | - Qi Wang
- College of Life SciencesBeijing Normal UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
| | - Dan‐Yang Yuan
- National Institute of Biological SciencesBeijingChina
| | | | - Yin‐Na Su
- National Institute of Biological SciencesBeijingChina
| | - Lin Li
- National Institute of Biological SciencesBeijingChina
| | - She Chen
- National Institute of Biological SciencesBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical ResearchTsinghua UniversityBeijingChina
| | - Xin‐Jian He
- College of Life SciencesBeijing Normal UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical ResearchTsinghua UniversityBeijingChina
| |
Collapse
|
4
|
Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
Collapse
Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| |
Collapse
|
5
|
Zhu TT, Sun CJ, Liu XY, Zhang JZ, Hou XB, Ni R, Zhang J, Cheng AX, Lou HX. Interaction of PKR with STCS1: an indispensable step in the biosynthesis of lunularic acid in Marchantia polymorpha. THE NEW PHYTOLOGIST 2023; 237:515-531. [PMID: 36062450 DOI: 10.1111/nph.18408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Unlike bibenzyls derived from the vascular plants, lunularic acid (LA), a key precursor for macrocyclic bisbibenzyl synthesis in nonvascular liverworts, exhibits the absence of one hydroxy group within the A ring. It was hypothesized that both polyketide reductase (PKR) and stilbenecarboxylate synthase 1 (STCS1) were involved in the LA biosynthesis, but the underlined mechanisms have not been clarified. This study used bioinformatics analysis with molecular, biochemical and physiological approaches to characterize STCS1s and PKRs involved in the biosynthesis of LA. The results indicated that MpSTCS1s from Marchantia polymorpha catalyzed both C2→C7 aldol-type and C6→C1 Claisen-type cyclization using dihydro-p-coumaroyl-coenzyme A (CoA) and malonyl-CoA as substrates to yield a C6-C2-C6 skeleton of dihydro-resveratrol following decarboxylation and the C6-C3-C6 type of phloretin in vitro. The protein-protein interaction of PKRs with STCS1 (PPI-PS) was revealed and proved essential for LA accumulation when transiently co-expressed in Nicotiana benthamiana. Moreover, replacement of the active domain of STCS1 with an 18-amino-acid fragment from the chalcone synthase led to the PPI-PS greatly decreasing and diminishing the formation of LA. The replacement also increased the chalcone formation in STCS1s. Our results highlight a previously unrecognized PPI in planta that is indispensable for the formation of LA.
Collapse
Affiliation(s)
- Ting-Ting Zhu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xin-Yan Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jiao-Zhen Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xu-Ben Hou
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Rong Ni
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jing Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| |
Collapse
|
6
|
Kisnieriene V, Trębacz K, Pupkis V, Koselski M, Lapeikaite I. Evolution of long-distance signalling upon plant terrestrialization: comparison of action potentials in Characean algae and liverworts. ANNALS OF BOTANY 2022; 130:457-475. [PMID: 35913486 PMCID: PMC9510943 DOI: 10.1093/aob/mcac098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND In this review, we summarize data concerning action potentials (APs) - long-distance electrical signals in Characean algae and liverworts. These lineages are key in understanding the mechanisms of plant terrestrialization. Liverworts are postulated to be pioneer land plants, whereas aquatic charophytes are considered the closest relatives to land plants. The drastic change of the habitat was coupled with the adaptation of signalling systems to the new environment. SCOPE APs fulfil the 'all-or-nothing' law, exhibit refractory periods and propagate with a uniform velocity. Their ion mechanism in the algae and liverworts consists of a Ca2+ influx (from external and internal stores) followed by/coincident with a Cl- efflux, which both evoke the membrane potential depolarization, and a K+ efflux leading to repolarization. The molecular identity of ion channels responsible for these fluxes remains unknown. Publication of the Chara braunii and Marchantia polymorpha genomes opened up new possibilities for studying the molecular basis of APs. Here we present the list of genes which can participate in AP electrogenesis. We also point out the differences between these plant species, e.g. the absence of Ca2+-permeable glutamate receptors (GLRs) and Cl--permeable SLAC1 channel homologues in the Chara genome. Both these channels play a vital role in long-distance signalling in liverworts and vascular plants. Among the common properties of APs in liverworts and higher plants is their duration (dozens of seconds) and the speed of propagation (mm s-1), which are much slower than in the algae (seconds, and dozens of mm s-1, respectively). CONCLUSIONS Future studies with combined application of electrophysiological and molecular techniques should unravel the ion channel proteins responsible for AP generation, their regulation and transduction of those signals to physiological responses. This should also help to understand the adaptation of the signalling systems to the land environment and further evolution of APs in vascular plants.
Collapse
Affiliation(s)
| | | | - Vilmantas Pupkis
- Department of Neurobiology and Biophysics, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio Ave, Vilnius, Lithuania
| | - Mateusz Koselski
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Akademicka, Lublin, Poland
| | - Indre Lapeikaite
- Department of Neurobiology and Biophysics, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio Ave, Vilnius, Lithuania
| |
Collapse
|
7
|
Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
Collapse
Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Imran S, Oyama M, Horie R, Kobayashi NI, Costa A, Kumano R, Hirata C, Tran STH, Katsuhara M, Tanoi K, Kohchi T, Ishizaki K, Horie T. Distinct Functions of the Atypical Terminal Hydrophilic Domain of the HKT Transporter in the Liverwort Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2022; 63:802-816. [PMID: 35380735 DOI: 10.1093/pcp/pcac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
K+/Na+ homeostasis is important for land plants, particularly under salt stress. In this study, the structure and ion transport properties of the high-affinity K+ transporter (HKT) of the liverwort Marchantia polymorpha were investigated. Only one HKT gene, MpHKT1, was identified in the genome of M. polymorpha. Phylogenetic analysis of HKT proteins revealed that non-seed plants possess HKTs grouped into a clade independent of the other two clades including HKTs of angiosperms. A distinct long hydrophilic domain was found in the C-terminus of MpHKT1. Complementary DNA (cDNA) of truncated MpHKT1 (t-MpHKT1) encoding the MpHKT_Δ596-812 protein was used to examine the functions of the C-terminal domain. Both MpHKT1 transporters fused with enhanced green fluorescent protein at the N-terminus were localized to the plasma membrane when expressed in rice protoplasts. Two-electrode voltage clamp experiments using Xenopus laevis oocytes indicated that MpHKT1 mediated the transport of monovalent alkali cations with higher selectivity for Na+ and K+, but truncation of the C-terminal domain significantly reduced the transport activity with a decrease in the Na+ permeability. Overexpression of MpHKT1 or t-MpHKT1 in M. polymorpha conferred accumulation of higher Na+ levels and showed higher Na+ uptake rates, compared to those of wild-type plants; however, phenotypes with t-MpHKT1 were consistently weaker than those with MpHKT1. Together, these findings suggest that the hydrophilic C-terminal domain plays a unique role in the regulation of transport activity and ion selectivity of MpHKT1.
Collapse
Affiliation(s)
- Shahin Imran
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046 Japan
- Department of Agronomy, Khulna Agricultural University, Khulna 9100, Bangladesh
| | - Masumi Oyama
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano, 386-8567 Japan
| | - Rie Horie
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano, 386-8567 Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Alex Costa
- Department of Biosciences, University of Milan, Via Celoria 26, Milano 20133, Italy
- Institute of Biophysics, National Research Council of Italy (CNR), Milano 20133, Italy
| | - Ryosuke Kumano
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano, 386-8567 Japan
| | - Chiho Hirata
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501 Japan
| | - Sen Thi Huong Tran
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046 Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, Hue, Thua Thien Hue 530000, Vietnam
| | - Maki Katsuhara
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046 Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | | | - Tomoaki Horie
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano, 386-8567 Japan
| |
Collapse
|
9
|
Matilla AJ. The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010020. [PMID: 35009023 PMCID: PMC8747232 DOI: 10.3390/plants11010020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.
Collapse
Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| |
Collapse
|
10
|
Genome-Wide Analysis of the Auxin/Indoleacetic Acid Gene Family and Response to Indole-3-Acetic Acid Stress in Tartary Buckwheat ( Fagopyrum tataricum). Int J Genomics 2021; 2021:3102399. [PMID: 34746298 PMCID: PMC8564212 DOI: 10.1155/2021/3102399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/17/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Auxin/indoleacetic acid (Aux/IAA) family genes respond to the hormone auxin, which have been implicated in the regulation of multiple biological processes. In this study, all 25 Aux/IAA family genes were identified in Tartary buckwheat (Fagopyrum tataricum) by a reiterative database search and manual annotation. Our study provided comprehensive information of Aux/IAA family genes in buckwheat, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. Aux/IAA family genes were nonuniformly distributed in the buckwheat chromosomes and divided into seven groups by phylogenetic analysis. Aux/IAA family genes maintained a certain correlation and a certain species-specificity through evolutionary analysis with Arabidopsis and other grain crops. In addition, all Aux/IAA genes showed a complex response pattern under treatment of indole-3-acetic acid (IAA). These results provide valuable reference information for dissecting function and molecular mechanism of Aux/IAA family genes in buckwheat.
Collapse
|
11
|
Singh M, Nara U, Kumar A, Choudhary A, Singh H, Thapa S. Salinity tolerance mechanisms and their breeding implications. J Genet Eng Biotechnol 2021; 19:173. [PMID: 34751850 PMCID: PMC8578521 DOI: 10.1186/s43141-021-00274-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/26/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND The era of first green revolution brought about by the application of chemical fertilizers surely led to the explosion of food grains, but left behind the notable problem of salinity. Continuous application of these fertilizers coupled with fertilizer-responsive crops make the country self-reliant, but continuous deposition of these led to altered the water potential and thus negatively affecting the proper plant functioning from germination to seed setting. MAIN BODY Increased concentration of anion and cations and their accumulation and distribution cause cellular toxicity and ionic imbalance. Plants respond to salinity stress by any one of two mechanisms, viz., escape or tolerate, by either limiting their entry via root system or controlling their distribution and storage. However, the understanding of tolerance mechanism at the physiological, biochemical, and molecular levels will provide an insight for the identification of related genes and their introgression to make the crop more resilient against salinity stress. SHORT CONCLUSION Novel emerging approaches of plant breeding and biotechnologies such as genome-wide association studies, mutational breeding, marker-assisted breeding, double haploid production, hyperspectral imaging, and CRISPR/Cas serve as engineering tools for dissecting the in-depth physiological mechanisms. These techniques have well-established implications to understand plants' adaptions to develop more tolerant varieties and lower the energy expenditure in response to stress and, constitutively fulfill the void that would have led to growth resistance and yield penalty.
Collapse
Affiliation(s)
- Mandeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Usha Nara
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Antul Kumar
- Department of Botany, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anuj Choudhary
- Department of Botany, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Hardeep Singh
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Sittal Thapa
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| |
Collapse
|
12
|
Fan H, Wei G, Chen X, Guo H, Crandall-Stotler B, Köllner TG, Chen F. Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm. PHYTOCHEMISTRY 2021; 190:112847. [PMID: 34237478 DOI: 10.1016/j.phytochem.2021.112847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Liverworts (Marchantiophyta) are among the earliest diverging lineages of extant land plants. Among their unique features, most liverworts contain membrane-bound oil bodies, organelles that accumulate diverse secondary metabolites, especially terpenoids. In contrast to the rich information on liverwort terpenoid chemistry, little is known about their biosynthesis. Recently, terpenoid biosynthesis was studied in a model thalloid species Marchantiapolymorpha, in which sesquiterpenes and monoterpenes are biosynthesized by a new type of terpene synthases termed microbial terpene synthase-like (MTPSL) proteins. Here we study terpenoid biosynthesis in a leafy liverwort Radula lindenbergiana. Vegetative plants of R.lindenbergiana were found to contain a mixture of sesquiterpenes, with (E,E)-α-farnesene/β-curcumene and (Z)-β-bisabolene being the most abundant constituents. From the analysis of the R. lindenbergiana transcriptome, five full-length MTPSL genes were identified. They were designated RlMTPSL1-5, respectively. Recombinant RlMTPSL proteins were produced in Escherichia coli and tested for sesquiterpene synthase activities using farnesyl diphosphate (FPP) as substrate. All except RlMTPSL5 were demonstrated to catalyze the formation of different sesquiterpenes. RlMTPSL1 produced multiple sesquiterpenes with eremophilene and an unidentified sesquiterpene as major products. The major products of RlMTPSL2 and RlMTPSL3 were β-elemene and an unidentified sesquiterpene, respectively. RlMTPSL4 was also a multi-product sesquiterpene synthase with an unidentified sesquiterpene being the major product. Homology-based structural modeling was performed to understand the structural basis underlying different product profiles of the RlMTPSLs proteins. Most of the sesquiterpene products of the four active RlMTPSLs were also detected in R. lindenbergiana plants. Expression levels of the four RlMTPSL genes encoding active enzymes in vegetative plants were compared. In phylogenetic analysis, RlMTPSL genes were found to cluster together, indicating lineage-specific expansion of MTPSL genes in lineages leading to R.lindenbergiana and M. polymorpha. This study strengthens evidence for the contribution of MTPSL genes to terpenoid biosynthesis in liverworts.
Collapse
Affiliation(s)
- Honghong Fan
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA; School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Guo Wei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Tobias G Köllner
- Department of Biochemistry, Max-Planck-Institute for Chemical Ecology, Hans-Knöll Str. 8, D-07745, Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
| |
Collapse
|
13
|
Pan L, Fonseca De Lima CF, Vu LD, De Smet I. A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage. FRONTIERS IN PLANT SCIENCE 2021; 12:650171. [PMID: 34484252 PMCID: PMC8415026 DOI: 10.3389/fpls.2021.650171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green algae and land plants. From that, we inferred the evolutionary relationships of MAP4K proteins through a phylogenetic reconstruction. Furthermore, we provided a classification of the MAP4Ks in the green lineage into three distinct.
Collapse
Affiliation(s)
- Lixia Pan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca De Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|
14
|
Furumizu C, Krabberød AK, Hammerstad M, Alling RM, Wildhagen M, Sawa S, Aalen RB. The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling. THE PLANT CELL 2021; 33:2915-2934. [PMID: 34240188 PMCID: PMC8462819 DOI: 10.1093/plcell/koab173] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in non-angiosperms. These discoveries provoke questions regarding co-evolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.
Collapse
Affiliation(s)
- Chihiro Furumizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Anders K Krabberød
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, Norway
| | - Renate M Alling
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Mari Wildhagen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Reidunn B Aalen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| |
Collapse
|
15
|
Koselski M, Pupkis V, Hashimoto K, Lapeikaite I, Hanaka A, Wasko P, Plukaite E, Kuchitsu K, Kisnieriene V, Trebacz K. Impact of Mammalian Two-Pore Channel Inhibitors on Long-Distance Electrical Signals in the Characean Macroalga Nitellopsis obtusa and the Early Terrestrial Liverwort Marchantia polymorpha. PLANTS 2021; 10:plants10040647. [PMID: 33805421 PMCID: PMC8067100 DOI: 10.3390/plants10040647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
Inhibitors of human two-pore channels (TPC1 and TPC2), i.e., verapamil, tetrandrine, and NED-19, are promising medicines used in treatment of serious diseases. In the present study, the impact of these substances on action potentials (APs) and vacuolar channel activity was examined in the aquatic characean algae Nitellopsis obtusa and in the terrestrial liverwort Marchantia polymorpha. In both plant species, verapamil (20-300 µM) caused reduction of AP amplitudes, indicating impaired Ca2+ transport. In N. obtusa, it depolarized the AP excitation threshold and resting potential and prolonged AP duration. In isolated vacuoles of M. polymorpha, verapamil caused a reduction of the open probability of slow vacuolar SV/TPC channels but had almost no effect on K+ channels in the tonoplast of N. obtusa. In both species, tetrandrine (20-100 µM) evoked a pleiotropic effect: reduction of resting potential and AP amplitudes and prolongation of AP repolarization phases, especially in M. polymorpha, but it did not alter vacuolar SV/TPC activity. NED-19 (75 µM) caused both specific and unspecific effects on N. obtusa APs. In M. polymorpha, NED-19 increased the duration of repolarization. However, no inhibition of SV/TPC channels was observed in Marchantia vacuoles, but an increase in open probability and channel flickering. The results indicate an effect on Ca2+ -permeable channels governing plant excitation.
Collapse
Affiliation(s)
- Mateusz Koselski
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (M.K.); (A.H.); (P.W.)
| | - Vilmantas Pupkis
- Department of Neurobiology and Biophysics, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania; (V.P.); (I.L.); (E.P.)
| | - Kenji Hashimoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan; (K.H.); (K.K.)
| | - Indre Lapeikaite
- Department of Neurobiology and Biophysics, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania; (V.P.); (I.L.); (E.P.)
| | - Agnieszka Hanaka
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (M.K.); (A.H.); (P.W.)
| | - Piotr Wasko
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (M.K.); (A.H.); (P.W.)
| | - Egle Plukaite
- Department of Neurobiology and Biophysics, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania; (V.P.); (I.L.); (E.P.)
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan; (K.H.); (K.K.)
| | - Vilma Kisnieriene
- Department of Neurobiology and Biophysics, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania; (V.P.); (I.L.); (E.P.)
- Correspondence: (V.K.); (K.T.)
| | - Kazimierz Trebacz
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (M.K.); (A.H.); (P.W.)
- Correspondence: (V.K.); (K.T.)
| |
Collapse
|
16
|
Delaux PM, Schornack S. Plant evolution driven by interactions with symbiotic and pathogenic microbes. Science 2021; 371:371/6531/eaba6605. [PMID: 33602828 DOI: 10.1126/science.aba6605] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today's continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.
Collapse
Affiliation(s)
- Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Castanet Tolosan, France.
| | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge CB2 1LR, UK.
| |
Collapse
|
17
|
Rico-Reséndiz F, Cervantes-Pérez SA, Espinal-Centeno A, Dipp-Álvarez M, Oropeza-Aburto A, Hurtado-Bautista E, Cruz-Hernández A, Bowman JL, Ishizaki K, Arteaga-Vázquez MA, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation. Int J Mol Sci 2020; 21:ijms21218354. [PMID: 33171770 PMCID: PMC7672586 DOI: 10.3390/ijms21218354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/22/2023] Open
Abstract
Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1–SPX1 and STOP1–ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.
Collapse
Affiliation(s)
- Félix Rico-Reséndiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Sergio Alan Cervantes-Pérez
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
| | - Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Melissa Dipp-Álvarez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Araceli Oropeza-Aburto
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
| | - Enrique Hurtado-Bautista
- Molecular Biology and Microbial Ecology, Unidad Irapuato, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico;
| | - Andrés Cruz-Hernández
- Escuela de Agronomía, Universidad de La Salle Bajío, León 37160, Guanajuato, Mexico;
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
| | | | - Mario A. Arteaga-Vázquez
- Group of Epigenetics and Developmental Biology, Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa 91640, Mexico;
| | - Luis Herrera-Estrella
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
- Correspondence: ; Tel.: +52-462-166-3000 (ext. 3005)
| |
Collapse
|
18
|
Schluttenhofer C. Origin and evolution of jasmonate signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110542. [PMID: 32771155 DOI: 10.1016/j.plantsci.2020.110542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
Jasmonate (JA) signaling is a key mediator of plant development and defense which arose during plants transition from an aqueous to terrestrial environment. Elucidating the evolution of JA signaling is important for understanding plant development, defense, and production of specialized metabolites. The lineage of key protein domains characterizing JA signaling factors was traced to identify the origins of CORONITINE INSENSITIVE 1 (COI1), JASMONATE ZIM-DOMAIN (JAZ), NOVEL INTERACTOR OF JAZ, MYC2, TOPLESS, and MEDIATOR SUBUNIT 25. Charophytes do not possess genes encoding key JA signaling components, including COI1, JAZ, MYC2, and the JAZ-interacting bHLH factors, yet their orthologs are present in bryophytes. TIFY family genes were found in charophyta and chlorophya algae. JAZs evolved from ZIM genes of the TIFY family through changes to several key amino acids. Dating placed the origin of JA signaling 515 to 473 million years ago during the middle Cambrian to early Ordovician periods. This time is known for rapid biodiversification and mass extinction events. An increased predation from the diversifying and changing fauna may have driven evolution of JA signaling and plant defense.
Collapse
Affiliation(s)
- Craig Schluttenhofer
- Agriculture Research and Development Program, 1400 Brush Row Road, Wilberforce OH, 45384, USA.
| |
Collapse
|
19
|
A mycorrhizae-like gene regulates stem cell and gametophore development in mosses. Nat Commun 2020; 11:2030. [PMID: 32332755 PMCID: PMC7181705 DOI: 10.1038/s41467-020-15967-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/02/2020] [Indexed: 12/14/2022] Open
Abstract
Plant colonization of land has been intimately associated with mycorrhizae or mycorrhizae-like fungi. Despite the pivotal role of fungi in plant adaptation, it remains unclear whether and how gene acquisition following fungal interaction might have affected the development of land plants. Here we report a macro2 domain gene in bryophytes that is likely derived from Mucoromycota, a group that includes some mycorrhizae-like fungi found in the earliest land plants. Experimental and transcriptomic evidence suggests that this macro2 domain gene in the moss Physcomitrella patens, PpMACRO2, is important in epigenetic modification, stem cell function, cell reprogramming and other processes. Gene knockout and over-expression of PpMACRO2 significantly change the number and size of gametophores. These findings provide insights into the role of fungal association and the ancestral gene repertoire in the early evolution of land plants.
Collapse
|
20
|
Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. The hornwort genome and early land plant evolution. NATURE PLANTS 2020; 6:107-118. [PMID: 32042158 PMCID: PMC7027989 DOI: 10.1038/s41477-019-0588-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
Collapse
Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xing Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Yan-Long Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Zhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Jian-Fen Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| |
Collapse
|
21
|
Yang Q, Niu X, Tian X, Zhang X, Cong J, Wang R, Zhang G, Li G. Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. BMC Genomics 2020; 21:12. [PMID: 31900112 PMCID: PMC6942412 DOI: 10.1186/s12864-019-6389-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 12/12/2019] [Indexed: 01/24/2023] Open
Abstract
Background Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which sub-divided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. Conclusion These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future.
Collapse
Affiliation(s)
- Qi Yang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaocui Niu
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaona Tian
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiujuan Zhang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Jingyu Cong
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruigang Wang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Guosheng Zhang
- Forestry College, Inner Mongolia Agricultural University, Hohhot, China.
| | - Guojing Li
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.
| |
Collapse
|
22
|
Yasui Y, Tsukamoto S, Sugaya T, Nishihama R, Wang Q, Kato H, Yamato KT, Fukaki H, Mimura T, Kubo H, Theres K, Kohchi T, Ishizaki K. GEMMA CUP-ASSOCIATED MYB1, an Ortholog of Axillary Meristem Regulators, Is Essential in Vegetative Reproduction in Marchantia polymorpha. Curr Biol 2019; 29:3987-3995.e5. [PMID: 31708390 DOI: 10.1016/j.cub.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/16/2019] [Accepted: 10/02/2019] [Indexed: 12/25/2022]
Abstract
A variety of plants in diverse taxa can reproduce asexually via vegetative propagation, in which clonal propagules with a new meristem(s) are generated directly from vegetative organs. A basal land plant, Marchantia polymorpha, develops clonal propagules, gemmae, on the gametophyte thallus from the basal epidermis of a specialized receptacle, the gemma cup. Here we report an R2R3-MYB transcription factor, designated GEMMA CUP-ASSOCIATED MYB1 (GCAM1), which is an essential regulator of gemma cup development in M. polymorpha. Targeted disruption of GCAM1 conferred a complete loss of gemma cup formation and gemma generation. Ectopic overexpression of GCAM1 resulted in formation of cell clumps, suggesting a function of GCAM1 in suppression of cell differentiation. Although gemma cups are a characteristic gametophyte organ for vegetative reproduction in a taxonomically restricted group of liverwort species, phylogenetic and interspecific complementation analyses support the orthologous relationship of GCAM1 to regulatory factors of axillary meristem formation, e.g., Arabidopsis REGULATOR OF AXILLARY MERISTEMS and tomato Blind, in angiosperm sporophytes. The present findings in M. polymorpha suggest an ancient acquisition of a transcriptional regulator for production of asexual propagules in the gametophyte and the use of the regulatory factor for diverse developmental programs, including axillary meristem formation, during land plant evolution.
Collapse
Affiliation(s)
- Yukiko Yasui
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Tomomi Sugaya
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto 390-8621, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Quan Wang
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Hidehiro Fukaki
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Tetsuro Mimura
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Hiroyoshi Kubo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto 390-8621, Japan
| | - Klaus Theres
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | |
Collapse
|
23
|
Dipp-Álvarez M, Cruz-Ramírez A. A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:17. [PMID: 30761165 PMCID: PMC6361745 DOI: 10.3389/fpls.2019.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 01/08/2019] [Indexed: 05/18/2023]
Abstract
Comparative genomics has revealed that members of early divergent lineages of land plants share a set of highly conserved transcription factors (TFs) with flowering plants. While gene copy numbers have expanded through time, it has been predicted that diversification, co-option, and reassembly of gene regulatory networks implicated in development are directly related to morphological innovations that led to more complex land plant bodies. Examples of key networks have been deeply studied in Arabidopsis thaliana, such as those involving the AINTEGUMENTA (ANT) gene family that encodes AP2-type TFs. These TFs play significant roles in plant development such as the maintenance of stem cell niches, the correct development of the embryo and the formation of lateral organs, as well as fatty acid metabolism. Previously, it has been hypothesized that the common ancestor of mosses and vascular plants encoded two ANT genes that later diversified in seed plants. However, algae and bryophyte sequences have been underrepresented from such phylogenetic analyses. To understand the evolution of ANT in a complete manner, we performed phylogenetic analyses of ANT protein sequences of representative species from across the Streptophyta clade, including algae, liverworts, and hornworts, previously unrepresented. Moreover, protein domain architecture, selection analyses, and regulatory cis elements prediction, allowed us to propose a scenario of how the evolution of ANT genes occurred. In this study we show that a duplication of a preANT-like gene in the ancestor of embryophytes may have given rise to the land plant-exclusive basalANT and euANT lineages. We hypothesize that the absence of euANT-type and basalANT-type sequences in algae, and its presence in extant land plant species, suggests that the divergence of pre-ANT into basal and eu-ANT clades in embryophytes may have influenced the conquest of land by plants, as ANT TFs play important roles in tolerance to desiccation and the establishment, maintenance, and development of complex multicellular structures which either became more complex or appeared in land plants.
Collapse
|
24
|
Furuya T, Kimori Y, Tsukaya H. A Method for Evaluating Three-Dimensional Morphological Features: A Case Study Using Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2019; 10:1214. [PMID: 31632430 PMCID: PMC6783815 DOI: 10.3389/fpls.2019.01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/03/2019] [Indexed: 05/13/2023]
Abstract
The description and evaluation of morphological features are essential to many biological studies. Bioimaging and quantification methods have been developed to analyze the morphological features of plants. However, efficient three-dimensional (3D) imaging and its quantification are still under development, particularly for studies of plant morphology, due to complex organ structure with great flexibility among individuals with the same genotype. In this study, we propose a new approach that combines a 3D imaging technique using micro-computed tomography and a mathematical image-processing method to describe 3D morphological features. As an example, we applied this method to Marchantia polymorpha, a new model plant used for the evolutional study of land plants, and we evaluated a mutant individual with an abnormal 3D shape. Using this new method, we quantitatively described the thallus morphology of M. polymorpha and distinguished the wild type from a mutant with different morphological features. Our newly established method can be applied to various tissues or bodies with irregular 3D morphology.
Collapse
Affiliation(s)
- Tomoyuki Furuya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan
- Department of Management and Information Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- ExCELLS, National Institutes of Natural Sciences, Okazaki, Japan
- *Correspondence: Dr. Hirokazu Tsukaya,
| |
Collapse
|
25
|
Norizuki T, Kanazawa T, Minamino N, Tsukaya H, Ueda T. Marchantia polymorpha, a New Model Plant for Autophagy Studies. FRONTIERS IN PLANT SCIENCE 2019; 10:935. [PMID: 31379911 PMCID: PMC6652269 DOI: 10.3389/fpls.2019.00935] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/03/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a catabolic process for bulk and selective degradation of cytoplasmic components in the vacuole/lysosome. In Saccharomyces cerevisiae, ATG genes were identified as essential genes for autophagy, and most ATG genes are highly conserved among eukaryotes, including plants. Although reverse genetic analyses have revealed that autophagy is involved in responses to abiotic and biotic stresses in land plants, our knowledge of its molecular mechanism remains limited. This limitation is partly because of the multiplication of some ATG genes, including ATG8, in widely used model plants such as Arabidopsis thaliana, which adds complexity to functional studies. Furthermore, due to limited information on the composition and functions of the ATG genes in basal land plants and charophytes, it remains unclear whether multiplication of ATG genes is associated with neofunctionalization of these genes. To gain insight into the diversification of ATG genes during plant evolution, we compared the composition of ATG genes in plants with a special focus on a liverwort and two charophytes, which have not previously been analyzed. Our results showed that the liverwort Marchantia polymorpha and the charophytes Klebsormidium nitens and Chara braunii harbor fundamental sets of ATG genes with low redundancy compared with those of A. thaliana and the moss Physcomitrella patens, suggesting that multiplication of ATG genes occurred during land plant evolution. We also attempted to establish an experimental system for analyzing autophagy in M. polymorpha. We generated transgenic plants expressing fluorescently tagged MpATG8 to observe its dynamics in M. polymorpha and produced autophagy-defective mutants by genome editing using the CRISPR/Cas9 system. These tools allowed us to demonstrate that MpATG8 is transported into the vacuole in an MpATG2-, MpATG5-, and MpATG7-dependent manner, suggesting that fluorescently tagged MpATG8 can be used as an autophagosome marker in M. polymorpha. M. polymorpha can provide a powerful system for studying the mechanisms and evolution of autophagy in plants.
Collapse
Affiliation(s)
- Takuya Norizuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- *Correspondence: Takashi Ueda,
| |
Collapse
|
26
|
Furuya T, Hattori K, Kimori Y, Ishida S, Nishihama R, Kohchi T, Tsukaya H. ANGUSTIFOLIA contributes to the regulation of three-dimensional morphogenesis in the liverwort Marchantia polymorpha. Development 2018; 145:dev.161398. [PMID: 30126903 DOI: 10.1242/dev.161398] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 08/06/2018] [Indexed: 01/04/2023]
Abstract
Arabidopsis thaliana mutants deficient in ANGUSTIFOLIA (AN) exhibit several phenotypes at the sporophyte stage, such as narrow and thicker leaves, trichomes with two branches, and twisted fruits. It is thought that these phenotypes are caused by abnormal arrangement of cortical microtubules (MTs). AN homologs are present in the genomes of diverse land plants, including the basal land plant Marchantia polymorpha, and their molecular functions have been shown to be evolutionarily conserved in terms of the ability to complement the A. thaliana an-1 mutation. However, the roles of ANs in bryophytes, the life cycle of which includes a dominant haploid gametophyte generation, remain unknown. Here, we have examined the roles of AN homologs in the model bryophyte M. polymorpha (MpAN). Mpan knockout mutants showed abnormal twisted thalli and suppressed thallus growth along the growth axis. Under weak blue light conditions, elongated thallus growth was observed in wild-type plants, whereas it was suppressed in the mutants. Moreover, disordered cortical MT orientations were observed. Our findings suggest that MpAN contributes to three-dimensional morphogenesis by regulating cortical MT arrangement in the gametophytes of bryophytes.
Collapse
Affiliation(s)
- Tomoyuki Furuya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Koro Hattori
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Sakiko Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan .,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| |
Collapse
|
27
|
Kubo H, Nozawa S, Hiwatashi T, Kondou Y, Nakabayashi R, Mori T, Saito K, Takanashi K, Kohchi T, Ishizaki K. Biosynthesis of riccionidins and marchantins is regulated by R2R3-MYB transcription factors in Marchantia polymorpha. JOURNAL OF PLANT RESEARCH 2018; 131:849-864. [PMID: 29845372 DOI: 10.1007/s10265-018-1044-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/07/2018] [Indexed: 05/21/2023]
Abstract
R2R3-MYB transcription factors constitute the largest gene family among plant transcription factor families. They became largely divergent during the evolution of land plants and regulate various biological processes. The functions of R2R3-MYBs are mostly characterized in seed plants but are poorly understood in non-seed plants. Here, we examined the function of two R2R3-MYB genes of Marchantia polymorpha (Mapoly0073s0038 and Mapoly0006s0226) that are closely related to subgroup 4 of the R2R3-MYB family. We performed LC/MS/MS metabolomics, RNA-seq analysis and expression analysis in overexpressors and knockout mutants of MpMYB14 and MpMYB02. Overexpression of MpMYB14 remarkably increased the amount of riccionidins, which are specific anthocyanins in liverworts and a few flowering plants. In contrast, overexpression of MpMYB02 increased the amount of several marchantins, which are characteristic cyclic bis (bibenzyl ether) compounds in M. polymorpha and related liverworts. Knockouts of MpMYB14 and MpMYB02 abolished the accumulation of riccionidins and marchantins, respectively. The expression of MpMYB14 was up-regulated by UV-B irradiation, N deficiency, and NaCl treatment, whereas the expression of MpMYB02 was down-regulated by NaCl treatment. Our results suggest that the regulatory framework of phenolic metabolism by R2R3-MYB was already established in early land plants.
Collapse
Affiliation(s)
- Hiroyoshi Kubo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, 390-8621, Japan.
| | - Shunsuke Nozawa
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, 390-8621, Japan
| | - Takuma Hiwatashi
- Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Youichi Kondou
- College of Science and Engineering, Kanto Gakuin University, Yokohama, 236-8501, Japan
| | - Ryo Nakabayashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, 230-0045, Japan
| | - Tetsuya Mori
- Center for Sustainable Resource Science, RIKEN, Yokohama, 230-0045, Japan
| | - Kazuki Saito
- Center for Sustainable Resource Science, RIKEN, Yokohama, 230-0045, Japan
- Graduate School of Pharmaceutical Science, Chiba University, Chiba, 260-8675, Japan
| | - Kojiro Takanashi
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, 390-8621, Japan
- Institute of Mountain Science, Shinshu University, Matsumoto, 390-8621, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | | |
Collapse
|
28
|
Benítez M, Hernández-Hernández V, Newman SA, Niklas KJ. Dynamical Patterning Modules, Biogeneric Materials, and the Evolution of Multicellular Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:871. [PMID: 30061903 PMCID: PMC6055014 DOI: 10.3389/fpls.2018.00871] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/04/2018] [Indexed: 05/18/2023]
Abstract
Comparative analyses of developmental processes across a broad spectrum of organisms are required to fully understand the mechanisms responsible for the major evolutionary transitions among eukaryotic photosynthetic lineages (defined here as the polyphyletic algae and the monophyletic land plants). The concepts of dynamical patterning modules (DPMs) and biogeneric materials provide a framework for studying developmental processes in the context of such comparative analyses. In the context of multicellularity, DPMs are defined as sets of conserved gene products and molecular networks, in conjunction with the physical morphogenetic and patterning processes they mobilize. A biogeneric material is defined as mesoscale matter with predictable morphogenetic capabilities that arise from complex cellular conglomerates. Using these concepts, we outline some of the main events and transitions in plant evolution, and describe the DPMs and biogeneric properties associated with and responsible for these transitions. We identify four primary DPMs that played critical roles in the evolution of multicellularity (i.e., the DPMs responsible for cell-to-cell adhesion, identifying the future cell wall, cell differentiation, and cell polarity). Three important conclusions emerge from a broad phyletic comparison: (1) DPMs have been achieved in different ways, even within the same clade (e.g., phycoplastic cell division in the Chlorophyta and phragmoplastic cell division in the Streptophyta), (2) DPMs had their origins in the co-option of molecular species present in the unicellular ancestors of multicellular plants, and (3) symplastic transport mediated by intercellular connections, particularly plasmodesmata, was critical for the evolution of complex multicellularity in plants.
Collapse
Affiliation(s)
- Mariana Benítez
- Centro de Ciencias de la Complejidad – Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Hernández-Hernández
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Lyon, France
| | - Stuart A. Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, United States
| | - Karl J. Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
29
|
Luo J, Zhou JJ, Zhang JZ. Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function. Int J Mol Sci 2018; 19:ijms19010259. [PMID: 29337875 PMCID: PMC5796205 DOI: 10.3390/ijms19010259] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 12/31/2022] Open
Abstract
Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive genes, including the Auxin/Indole-3-Acetic Acid (Aux/IAA) family, the auxin response factor (ARF) family, small auxin upregulated RNA (SAUR), and the auxin-responsive Gretchen Hagen3 (GH3) family. Aux/IAA proteins are short-lived nuclear proteins comprising several highly conserved domains that are encoded by the auxin early response gene family. These proteins have specific domains that interact with ARFs and inhibit the transcription of genes activated by ARFs. Molecular studies have revealed that Aux/IAA family members can form diverse dimers with ARFs to regulate genes in various ways. Functional analyses of Aux/IAA family members have indicated that they have various roles in plant development, such as root development, shoot growth, and fruit ripening. In this review, recently discovered details regarding the molecular characteristics, regulation, and protein-protein interactions of the Aux/IAA proteins are discussed. These details provide new insights into the molecular basis of the Aux/IAA protein functions in plant developmental processes.
Collapse
Affiliation(s)
- Jie Luo
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing-Jing Zhou
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|